I wouldn't rule out the possibility of shiny Zekrom\Reshiram entirely.
It's possible that the game just says "okay, if the PID would become shiny if you XOR'd with 0xSomeNumber, then make it shiny. And if the PID is already shiny, then AND it with 0x10000000."
This would make it possible to still have shiny Zekrom\Reshirams while thwarting people attempting the obvious - modifying the ID\SID so the PID would be shiny.
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